Merge pull request #1027 from sanger/python-version-upgradec

Update Python version in Dockerfile and Pipfile to 3.13

.github/workflows/ci.yml

@@ -16,14 +16,24 @@ env:
   SETTINGS_MODULE: crawler.config.test
 
 jobs:
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      python_version: ${{ steps.read_python_version.outputs.python_version }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Read Python version
+        id: read_python_version
+        run: echo "::set-output name=python_version::$(cat .python-version)"
   black:
     runs-on: ubuntu-latest
+    needs: setup
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: ${{ needs.setup.outputs.python_version }}
       - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
@@ -42,12 +52,13 @@ jobs:
           python -m black --check .
   flake8:
     runs-on: ubuntu-latest
+    needs: setup
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: ${{ needs.setup.outputs.python_version }}
       - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
@@ -66,12 +77,13 @@ jobs:
           flake8
   mypy:
     runs-on: ubuntu-latest
+    needs: setup
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: ${{ needs.setup.outputs.python_version }}
       - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
@@ -89,6 +101,7 @@ jobs:
           python -m mypy .
   test:
     runs-on: ubuntu-latest
+    needs: setup
     services:
       mysql:
         image: mysql:8.0
@@ -102,7 +115,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: ${{ needs.setup.outputs.python_version }}
       - uses: actions/cache@v4
         with:
           path: ~/.cache/pip

.gitignore

@@ -87,9 +87,6 @@ target/
 profile_default/
 ipython_config.py
 
-# pyenv
-.python-version
-
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
 #   However, in case of collaboration, if having platform-specific dependencies or dependencies
@@ -139,3 +136,6 @@ dmypy.json
 
 # RabbitMQ admin tool
 rabbitmqadmin
+
+# PyCharm indexes
+.idea

.python-version

@@ -0,0 +1 @@
+3.13.0

Dockerfile

@@ -1,6 +1,6 @@
 # Use buster for a smaller image size and install only the required packages.
 # Note that bullseye uses Debian 11 which cannot install msodbcsql17.
-FROM python:3.8-slim-buster
+FROM python:3.13-slim
 
 # > Setting PYTHONUNBUFFERED to a non empty value ensures that the python output is sent straight to
 # > terminal (e.g. your container log) without being first buffered and that you can see the output

Pipfile

@@ -36,7 +36,7 @@ sqlalchemy = "~=2.0"
 lab-share-lib = { git = 'https://github.com/sanger/lab-share-lib.git', ref = 'v0.2.0', editable = false }
 
 [requires]
-python_version = "3.8"
+python_version = "3.13"
 
 [pipenv]
 allow_prereleases = true

crawler/db/mysql.py

@@ -245,7 +245,7 @@ def reset_is_current_flags(
         cursor.execute(sql_statement, [datetime.now()] + rna_ids_group)
         total_rows_affected += cursor.rowcount
 
-    logger.info(f"Reset is_current to false for { total_rows_affected } rows.")
+    logger.info(f"Reset is_current to false for {total_rows_affected} rows.")
 
 
 def insert_or_update_samples_in_mlwh(

migrations/back_populate_uuids_date_range.py

@@ -123,7 +123,7 @@ def update_mongo(config: Config, updated_at: datetime) -> None:
                 counter += 1
 
             if counter > 0 and (counter % 5000) == 0:
-                logger.debug(f"{counter = }")
+                logger.debug(f"{counter=}")
 
         logger.debug(f"{counter} samples updated in mongo")
 

tests/helpers/test_cherrypicker_data_helper.py

@@ -44,7 +44,7 @@ def test_create_barcodes(config, count):
     ) as generate_barcodes:
         actual = create_barcodes(config, count)
 
-    assert generate_barcodes.called_with(count)
+    generate_barcodes.assert_called_with(config, "TEST", count)
     assert actual == expected